Chapter 1 Getting started

R is a statistical environment and programming language for data analysis and graphical display. The software is open-source, freely available and has been compiled ready for use on Windows, Mac and Linux computers. The Bioconductor framework has a considerable number of packages that have been implemented for the analysis and exploration of metabolomics, proteomics, DNA microarray and Next Generation DNA sequence data.

This workshop is intended as an introduction to R that should familiarise you with the concepts that underpin the crafting of workflows in R and some of the key techniques that will aid in the crafting of reusable workflows.

Some of the topics we will cover over the course of the day include:

• Using the RStudio IDE for running a data analysis in R
• The basics of literate programming for studies using R
• Loading, creating, modifying and saving basic -omics data objects according to key formats
• Create graphs and plots of data
• Understanding how to read and understand someone else’s R-code